1Z8D

Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7GPBPDB ENTRY 7GPB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9277PEG mme 550, glucose, TRIS, spermine, DTT, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.140.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.37α = 90
b = 144β = 90
c = 59.44γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.0NSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2876.797.50.06811.43.5365213652111.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.3693.10.20152.93434

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 7GPB2.330.79353343533470698.10.1920.251RANDOM17.3
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
3.95-1.38-2.57
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.4
c_scangle_it2.71
c_scbond_it1.91
c_mcangle_it1.74
c_angle_deg1.4
c_mcbond_it1.14
c_improper_angle_d0.95
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.4
c_scangle_it2.71
c_scbond_it1.91
c_mcangle_it1.74
c_angle_deg1.4
c_mcbond_it1.14
c_improper_angle_d0.95
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6707
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms45

Software

Software
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing